The laboratory studies conformational properties of the most important molecule in Nature - DNA. DNA can exist in conformations substantially different from the classical Watson-Crick double helix. Its structure can vary from the anti-parallel Watson-Crick helix in minor ways like nucleotide geometry, but can also vary significantly in parameters including double-helix handedness, orientation of strands, type of base pairing, and the number of associated strands. The capability of particular nucleotide motifs to adopt specific conformations is critical for their recognition by other molecules, especially proteins, and underlies genome translocations connected with diseases. Mapping of the conformational properties of the nucleotide motifs that occur in the human genome is one goal of post-genomic biophysics and structural biology. These analyses assign properties to the genomic nucleotide sequences that are closer to their function than the nucleotide sequences themselves. The biological information carried by the 98% of the human genome that does not code for proteins is still very far from being understood. Interestingly, the "noncoding" regions are frequently formed by simple repetitive sequences of nucleotides that are especially prone to adopt non-Watson-Crick DNA duplex conformations. Unusual conformations have been shown to be critical in both normal and pathological phenomena, including replication, transcription, differentiation, aging and various types of cancer.
For many years, the laboratory has been interested in the conformations adopted by simple, but biologically relevant, sequence repeats. For example, expansion of certain trinucleotide repeats correlates with numerous human diseases. These pathological expansions include the (CAG)n/(CTG)n sequences linked to Huntington,s and Kennedy,s diseases, myotonic dystrophy, spinocerebellar ataxia and others; the (CCG)n/(CGG)n sequences connected with fragile X syndrome; and the (AAG)n/(CTT)nsequences that play a role in Friedreich,s ataxia. In recent years, we have been interested in G/C rich DNA regions that form guanine or intercalated cytosine quadruplexes under certain conditions. The human genome contains thousands of places where the primary structure is prone to adopt the quadruplex structure. This unusual DNA arrangement is extremely important at chromosome ends and may be involved in control of gene expression.
Our goal is to find the dependence of DNA conformational properties on the nucleotide sequence. The main method used is electronic circular dichroism spectroscopy: Circular dichroism (CD) is a phenomenon originating from different absorption of right-handed and left-handed circularly polarized light by chiral molecules. One source of DNA chirality is the sugar carbon atom to which the heterocyclic base is attached in nucleosides. This effect, however, is less significant than the chirality originating from asymmetric stacking of absorbing bases into different helical arrangements. CD spectroscopy is extremely sensitive to changes in mutual position of bases and, therefore, it is uniquely suited to analysis of conformational isomerizations of nucleic acids in solution. The isomerizations include transitions from helix to coil, B to A, B to Z, Z to Z,, B to X, and A to X, formation ofguanine quadruplexes, cytosine-intercalated quadruplexes, and parallel duplexes, the duplex-hairpin transitions, and others (hyperlinks lead to example spectra).